Python MuscleCommandline.cluster1 примеры использования

Пример #1

Файл: 2.3-intradonor_analysis.py Проект: scharch/SONAR

def muscleProcess (threadID, filebase, outbase, treebase):

	fasta	 = filebase % threadID
	output	 = outbase  % threadID
	treeFile = treebase % threadID

	print( "Building NJ tree from %s" % fasta )

	run_muscle = MuscleCommandline( cmd=muscle, input=fasta, out=output )
	run_muscle.tree1      = treeFile
	run_muscle.cluster1   = "neighborjoining"
	run_muscle.maxiters   = 1
	thisVarHidesTheOutput = run_muscle()

Пример #2

def muscleProcess (threadID, filebase, outbase, treebase):

	fasta	 = filebase % threadID
	output	 = outbase  % threadID
	treeFile = treebase % threadID

	print( "Building NJ tree from %s" % fasta )

	run_muscle = MuscleCommandline( cmd=muscle, input=fasta, out=output )
	run_muscle.tree1      = treeFile
	run_muscle.cluster1   = "neighborjoining"
	run_muscle.maxiters   = 1
	thisVarHidesTheOutput = run_muscle()

Пример #3

Файл: 2.3-intradonor_analysis.py Проект: Batsi-2015/SONAR

	def run(self):
		run_muscle = MuscleCommandline( input=self.fasta, out=self.output )
		run_muscle.tree1      = self.tree
		run_muscle.cluster1   = "neighborjoining"
		run_muscle.maxiters   = 1
		thisVarHidesTheOutput = run_muscle()